rs1405793

Positions:

• chr3-39715025-A-C
• chr3-39715025-A-G
• chr3-39715025-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.361 in 151,982 control chromosomes in the GnomAD database, including 12,603 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (12603 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54823 AN: 151862 Hom.: 12557 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.326

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.361 AC: 54919 AN: 151982 Hom.: 12603 Cov.: 32 AF XY: 0.356 AC XY: 26448 AN XY: 74306

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.262

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.204

Gnomad4 SAS AF: 0.282

Gnomad4 FIN AF: 0.205

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.323

Alfa AF: 0.163 Hom.: 319

Bravo AF: 0.375

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.20
DANN	Benign	0.51

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1405793; hg19: chr3-39756516;